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Revealing how a biological network is organized to realize its function is one of the main topics in systems biology. The functional backbone network, defined as the primary structure of the biological network, is of great importance in maintaining the main function of the biological network. We propose a new algorithm, the tinker algorithm, to determine this core structure and apply it in the cell-cycle system. With this algorithm, the backbone network of the cell-cycle network can be determined accurately and efficiently in various models such as the Boolean model, stochastic model, and ordinary differential equation model. Results show that our algorithm is more efficient than that used in the previous research. We hope this method can be put into practical use in relevant future studies.
Complex networks provide us a new view for investigation of immune systems. In this paper we collect data through STRING database and present a model with cooperation network theory. The cytokine-protein network model we consider is constituted by tw
Network optimization strategies for the process of synchronization have generally focused on the re-wiring or re-weighting of links in order to: (1) expand the range of coupling strengths that achieve synchronization, (2) expand the basin of attracti
Complex biological functions are carried out by the interaction of genes and proteins. Uncovering the gene regulation network behind a function is one of the central themes in biology. Typically, it involves extensive experiments of genetics, biochem
The network of 5823 cities of Mexico with a population more than 5000 inhabitants is studied. Our analysis is focused to the spectral properties of the adjacency matrix, the small-world properties of the network, the distribution of the clustering co
Nuclear magnetic resonance (NMR) spectroscopy is a powerful method for the investigation of three-dimensional structures of biological molecules such as proteins. Determining a protein structure is essential for understanding its function and alterat